1Z2A

GDP-Bound Rab23 GTPase crystallized in P2(1)2(1)2(1) space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPolyalanine Rab3a

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP527715% PEG 6000, 50mM Na acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1441.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.281α = 90
b = 61.44β = 89.99
c = 63.854γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2004-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.95095.90.04424.54124821252234.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9679.40.2685.34834

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPolyalanine Rab3a1.98125221168460096.210.2430.23220.229820.27761RANDOM25.353
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.761.44-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.267
r_dihedral_angle_4_deg15.147
r_dihedral_angle_3_deg14.512
r_dihedral_angle_1_deg5.276
r_scangle_it1.67
r_angle_refined_deg1.085
r_scbond_it0.996
r_mcangle_it0.807
r_mcbond_it0.462
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.267
r_dihedral_angle_4_deg15.147
r_dihedral_angle_3_deg14.512
r_dihedral_angle_1_deg5.276
r_scangle_it1.67
r_angle_refined_deg1.085
r_scbond_it0.996
r_mcangle_it0.807
r_mcbond_it0.462
r_nbtor_refined0.294
r_nbd_refined0.177
r_symmetry_vdw_refined0.174
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.129
r_chiral_restr0.062
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1293
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing